SUNY has a partial implementation of something like what you're describing in our LMS, but we use it for a different purpose. Basically, an instructor can assign a comment and a grade to any student submission, including a discussion post. (The pedagogy we promote heavily emphasizes interactivity, so providing students with good feedback on how well they participate is key.) The instructor can either keep the comment and grade or share them with the individual student, and the grade rolls up automatically into our gradebook (or will do so when the gradebook is finished). We don't have the Flickr-like (or Annotea-like) annotation functionality that you described; however, our faculty are very hot on Flickr right now, so I suspect they'd be enthusiastic about the sticky note idea as well.
At any rate, this serves a different purpose than the functionality I suggested in my original post. The latter is more to organize class activities for the students. Our system has something we call a "course map." Think of it as being somewhat like the LORS interface, except that documents in the navigation tree can automagically be set up to link to a discussion thread, a test, etc. What this does is organize class activities--reading, discussions, tests, etc.--according to the sequence of learning experiences that the instructor wants to create rather than by software functionality--e.g., forums, file storage, etc. Hanging a discussion thread directly off of a document in the content repository is a step in that general direction.
Even more interesting might be the ability to trigger and link into other module functionality (again, discussion forums, evaluations, and the like) through the metadata associated with a learning object in LORS. When you upload the content, the system would see that the third document is associated with a discussion learning activity (for example) and generate the associated thread.
